<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<!-- DTD for polymer definitions, used by the
'massXpert' mass spectrometry application.
Copyright 2006,2007,2008 Filippo Rusconi
Licensed under the GNU GPL -->
<!DOCTYPE polchemdefinition [
<!ELEMENT polchemdefinition (polchemdefdata)>
<!ATTLIST polchemdefinition version NMTOKEN #REQUIRED>
<!ELEMENT polchemdefdata (name , leftcap , rightcap , codelen , ionizerule , monomers , modifs , crosslinkers , cleavageagents , fragmentationpathways)>
<!ELEMENT ionizerule (formula , charge , level)>
<!ELEMENT monomers (mnm)*>
<!ELEMENT modifs (mdf)*>
<!ELEMENT crosslinkers (clk)*>
<!ELEMENT cleavageagents (cla)*>
<!ELEMENT fragmentationpathways (fgp)*>
<!ELEMENT mnm (name , code , formula)>
<!ELEMENT mdf (name , formula , targets , maxcount)>
<!ELEMENT clk (name , formula , modifname*)>
<!ELEMENT cla (name , pattern , clr*)>
<!ELEMENT fgp (name , end , formula , sidechaincontrib , comment? , fgr*)>
<!ELEMENT clr (name , (le-mnm-code , le-formula)? , (re-mnm-code , re-formula)?)>
<!ELEMENT fgr (name , formula , prev-mnm-code? , curr-mnm-code? , next-mnm-code? , comment?)>
<!ELEMENT leftcap (#PCDATA)>
<!ELEMENT rightcap (#PCDATA)>
<!ELEMENT codelen (#PCDATA)>
<!ELEMENT charge (#PCDATA)>
<!ELEMENT maxcount (#PCDATA)>
<!ELEMENT level (#PCDATA)>
<!ELEMENT name (#PCDATA)>
<!ELEMENT modifname (#PCDATA)>
<!ELEMENT code (#PCDATA)>
<!ELEMENT formula (#PCDATA)>
<!ELEMENT sidechaincontrib (#PCDATA)>
<!ELEMENT targets (#PCDATA)>
<!ELEMENT pattern (#PCDATA)>
<!ELEMENT end (#PCDATA)>
<!ELEMENT le-mnm-code (#PCDATA)>
<!ELEMENT re-mnm-code (#PCDATA)>
<!ELEMENT le-formula (#PCDATA)>
<!ELEMENT re-formula (#PCDATA)>
<!ELEMENT comment (#PCDATA)>
<!ELEMENT prev-mnm-code (#PCDATA)>
<!ELEMENT curr-mnm-code (#PCDATA)>
<!ELEMENT next-mnm-code (#PCDATA)>
]>
<polchemdefinition version="2">
	<polchemdefdata>
		<name>dna</name>
		<leftcap>+OH</leftcap>
		<rightcap>+H</rightcap>
		<codelen>2</codelen>
		<ionizerule>
			<formula>-H</formula>
			<charge>1</charge>
			<level>1</level>
		</ionizerule>
		<monomers>
			<mnm>
				<name>Adenine</name>
				<code>A</code>
				<formula>C10H12N5O5P1</formula>
			</mnm>
			<mnm>
				<name>PS-Adenine</name>
				<code>Sa</code>
				<formula>C10H12N5O4P1S1</formula>
			</mnm>
			<mnm>
				<name>Guanine</name>
				<code>G</code>
				<formula>C10H12N5O6P1</formula>
			</mnm>
			<mnm>
				<name>PS-Guanine</name>
				<code>Sg</code>
				<formula>C10H12N5O5P1S1</formula>
			</mnm>
			<mnm>
				<name>Thymine</name>
				<code>T</code>
				<formula>C10H13N2O7P1</formula>
			</mnm>
			<mnm>
				<name>Uracile</name>
				<code>U</code>
				<formula>C9H11N2O8P1</formula>
			</mnm>
			<mnm>
				<name>PS-Thymine</name>
				<code>St</code>
				<formula>C10H13N2O6P1S1</formula>
			</mnm>
			<mnm>
				<name>Cytosine</name>
				<code>C</code>
				<formula>C9H12N3O6P1</formula>
			</mnm>
			<mnm>
				<name>PS-Cytosine</name>
				<code>Sc</code>
				<formula>C9H12N3O5P1S1</formula>
			</mnm>
		</monomers>
		<modifs>
			<mdf>
				<name>Dephosphorylate</name>
				<formula>-H1O3P1</formula>
				<targets>*</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>Phosphorothioate</name>
				<formula>S1-O1</formula>
				<targets>*</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>Hairpin-cytosine</name>
				<formula>C31H48N5O9S1</formula>
				<targets>*</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>Oxidation</name>
				<formula>O1</formula>
				<targets>;G;</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>Phosphorylation</name>
				<formula>H1O3P1</formula>
				<targets>!</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>DiPhosphorylation</name>
				<formula>H2O6P2</formula>
				<targets>!</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>Methylation</name>
				<formula>C1H1</formula>
				<targets>;C;</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>PhotoCleaveBiot</name>
				<formula>C25H35N5O5S1</formula>
				<targets>*</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>PhotCleavBiotPhosphoryl</name>
				<formula>C25H29N5O8P1S1</formula>
				<targets>*</targets>
				<maxcount>1</maxcount>
			</mdf>
		</modifs>
		<crosslinkers>
			<clk>
				<name>Thymine-dimer</name>
				<formula>-H1+H1</formula>
			</clk>
		</crosslinkers>
		<cleavageagents>
			<cla>
				<name>EcoRI</name>
				<pattern>G/AATTC</pattern>
			</cla>
			<cla>
				<name>HindIII</name>
				<pattern>A/AGCTT</pattern>
			</cla>
			<cla>
				<name>SacI</name>
				<pattern>GAGCT/C</pattern>
			</cla>
			<cla>
				<name>XhoI</name>
				<pattern>C/TCGAG</pattern>
			</cla>
		</cleavageagents>
		<fragmentationpathways>
			<fgp>
				<name>a</name>
				<end>LE</end>
				<formula>-OH</formula>
				<sidechaincontrib>0</sidechaincontrib>
			</fgp>
			<fgp>
				<name>a-B</name>
				<end>LE</end>
				<formula>-HOH+C5H8O5P</formula>
				<sidechaincontrib>-1</sidechaincontrib>
				<comment>abasic a fragment</comment>
			</fgp>
			<fgp>
				<name>b</name>
				<end>LE</end>
				<formula>+H</formula>
				<sidechaincontrib>0</sidechaincontrib>
			</fgp>
			<fgp>
				<name>c</name>
				<end>LE</end>
				<formula>+PO2</formula>
				<sidechaincontrib>0</sidechaincontrib>
			</fgp>
			<fgp>
				<name>d</name>
				<end>LE</end>
				<formula>+HPO3+H</formula>
				<sidechaincontrib>0</sidechaincontrib>
			</fgp>
			<fgp>
				<name>w</name>
				<end>RE</end>
				<formula>+OH</formula>
				<sidechaincontrib>0</sidechaincontrib>
			</fgp>
			<fgp>
				<name>x</name>
				<end>RE</end>
				<formula>-H</formula>
				<sidechaincontrib>0</sidechaincontrib>
			</fgp>
			<fgp>
				<name>y</name>
				<end>RE</end>
				<formula>-HPO2+H</formula>
				<sidechaincontrib>0</sidechaincontrib>
			</fgp>
			<fgp>
				<name>z</name>
				<end>RE</end>
				<formula>-HPO3-H</formula>
				<sidechaincontrib>0</sidechaincontrib>
			</fgp>
		</fragmentationpathways>
	</polchemdefdata>
</polchemdefinition>
